DNA Testing - know the In's and Out's of it. Genetic Genealogy, a new branch of genealogy combining genetics and traditional genealogy research, is the most accurate tool for the family historian. Family connections can be proven or disproven. DNA testing can support a paper trail which is often in question given the lack of surviving records. Its popularity grows daily with thousands testing monthly throughout the world.

01 March 2014

Big Y is rolling on...

My, oh my! The Big Y
is here!

Since the Family Tree DNAConference last November, thousands of Big Y tests have been ordered, but only 100 Big Y tests were released February 27th
with the remaining initial orders to be delivered over the next month. At that point the backlog should be resolved,
and the Big Y will keep rolling on...

The Big Y explores your deep ancestral lines and is intended
for those who are interested in discovering what SNPs appear on their
Y-chromosome. This extensive test uses next-generation sequencing and maps the SNP
positions. The Y-chromosome has about 60 million bases, but a large percentage
is inaccessible or cannot be reliably tested with today’s technology. The gold standard is said to be 10 million
bases, but the Big Y targets over 13 million and gets from 11.5 to 12.5 million
reads on the average. The Big Y tests
over 25,000 SNPs out of the 36,562 known Y-SNPs in the FTDNA database.

First, let’s back-up
and clarify what a SNP is:

A
single nucleotide polymorphism (SNP; pronounced snip) is the most common type of genetic variation in humans,
according to the Genetics Home Reference
website.
SNPs can be found throughout a person’s
DNA roughly one SNP in every 300 nucleotides on average. With 3 billion base
pairs in the human genome, that is about 10 million SNPs per human. Each SNP is
a form of mutation (change) and represents a difference in a single DNA
building block, called a nucleotide. For example, a SNP may result in the
replacement of the base cytosine (C) or guanine (G) with the base thymine (T)
or adenine (A) at a certain location on a chromosome. Generally, these
markers mutate only once, although back mutations or reversions (a situation
where a mutation results in the nucleotide being restored to its previous
condition at that location) do occur.

As a mutation is carried forward in the consecutive
generations, SNP markers help determine haplogroups for Y-chromosome DNA. For
genealogists, narrowing those haplogroups to detailed subclades (sub-branches)
is beneficial. It helps them determine
with whom in the general population they have a closer genetic relationship (a
match).

When a new SNP is found, a new haplogroup
subclade is determined, but before the geneticists declare a new haplogroup
subclade, a required minimum number of people must have the new SNP. This is
the major reason why some haplogroup project administrators will ask testers
from projects to test for a certain SNP. These haplogroup administrators wish
to increase the number of known testers for that SNP so the geneticists will
place it on the phylogenetic tree. All the descendants of the person with this
newly discovered SNP will carry that mutation, and that mutation defines that
new group.

Big Y Results

The customer’s personal web pages will contain two
tabs. The first is for reporting Known SNPs while the second is for Novel Variants; that is, the list of SNPs
not on the list of 36,582 known and previously names SNPs. So clearly, this test may produce some future
SNPs among some families or clans which are currently not recognized.

Known SNPs

The customer’s webpage for Known SNPs includes several columns: SNP Name, Derived?, On Y-Tree?, Reference, Genotype, Confidence. The default is 10 items shown at a time, but
more can be viewed. The lower left tells
you how many entries are in your result, stating something similar to “Showing
1 of 10 of 25,000 of 36,564”. All the
results are shown, both positive and negative so there is no question about
whether a specific location was tested, or its results. There is also the
option of a no-call or poor confidence call at that location.

The SNP Name column
is just the names of the SNPs listed alphabetically. You can search on the full
SNP name or a partial name.

The Derived? column
indicates whether the particular genotype is ancestral or derived. Derived means the individual is positive for
the SNP. There options to SHOW ALL, YES
(+), NO (-) or ?. The question mark
means the SNP is a no call, the SNP is not in the coverage region or there is not
enough data to determine its value.) The
default is YES.

On Y-Tree? column
indicates whether the SNP exists on the Y-chromosome phylogentic tree. The options to filter this column are: SHOW
ALL, YES, NO.

The Reference column
provides the nucleotide base (adenine, cytosine, thymine or guanine) as
indicated by the GRCh37 human reference genome which is maintained by the
Genome Reference Consortium. Those
options include: SHOW ALL, A, C, T, G

The Genotype column
is the tester’s nucleotide base at a given SNP potion. Those options include: SHOW ALL, A, C, T, G, ?. The question mark means the result is not
known.

The Confidence column
is a score that represents how confident FTDNA is in the accuracy of the data
for that SNP. Options include: SHOW ALL, HIGH (no question at that
location), MEDIUM (ok, but the bottom of the border line to be called high) and
UNKNOWN (not clear enough to call or no data).

Novel Variants

The second results page covers Novel Variants which are the list of SNPs that not on the list of
36,582 known and previously named SNPs.
These SNPs will be analyzed on an on-going basis in the case a SNP is significant
enough to be given a name and added to the Y-phylogenetic tree (Y-haplotree). However, some SNPs may remain novel and could
signify a private, family or clan variant.
Project administrators may submit these novel SNPs to be considered for
naming via the SNP Request form on
their GAP (Group Administrator Pages) website. However, getting these new SNPs
approved will take time.

This page provides columns for Position, Reference, Genotype and Confidence. These columns
are the same categories as above, but are for the SNPs not on the Y-haplotree. All novel mutations are being reported by a
reference number which can be compared to like data from any source.

There is also the following links on each page:

Help (refers you
to the FAQs on the topic, but FTDNA is transitioning to their Learning Center)

Haplotree (links
to your haplogtree page)

Y Reset (allows
you to rest the filters to the default filters)

Download Raw Data

Downloading the raw data cannot be done until sometime next
week. Files can be downloaded by using 3rd
party tools, VCF (Variant Call File) which is a tab-delimited system that can
be imported to Excel (A sample VCF file can be found in the 1000 Genomes Wiki)
and BEDfile which is a text file that shows a range of positions. BAM files will be available soon as the
delivery method is being finalized since the file is so large. Insertions and deletions are included in the
download files, but not reported on the customer’s results page.

Once all the customer data from this initial sale is loaded
into a huge database, the new SNPs that are found in enough of the population to
be named will be added to the Y-haplotree, and at that time, a customer who has
not taken the Big Y could order that particular SNP. Novel variants will remain
that, and will continue to be reported on client pages.

In about six weeks FTDNA will publish a paper on the average
number of novel SNPs per person which are being found, the mutation rates, and
findings.

HaploTree version 2014

The new Y-tree is coming, honest! The reason for the delay includes the “SNP tsunami”
as the Geno 2.0 has helped increase the size of the tree to about 8 times
larger than it was four years ago. The Big Y will increase it even more. Negative results for SNPs that are downstream
of the most terminal positive SNP will be included. For example L21+ on the R tree has 9
downstream SNPs which will be reported on the tree, even the negative result
for a tester. However, if there are no negative SNPs for an already terminal
SNP, there can be no further reporting as in the case of M222+. Future updates to the tree will record the
positive SNPs on your webpage.

Suggestions Welcomed!

If you have a suggestion for additional Big Y tools or
features, email Elise or Rebekah and they will forward the request to
management for consideration.

Once the results of the thousands of tests which have been ordered
are available, others who appear to have the same Y-SNP signature may wish to
order individual SNPs to determine their terminal SNP (last currently known SNP
on the Y-haplotree for which you test positive), but remember that 17 SNPs at
$39 each is the cost of the Big Y so confer with your haplogroup administrator
first. Once the backlog is cleared, the results can be expected in about 8-10
weeks. Order from Family Tree DNA.

No comments:

Emily Aulicino

Genetic Genealogist

Welcome to My Genetic Genealogy Blog

Genetic Genealogy is a wonderful resource for the family genealogist or historian and is growing daily! From time to time I will post URLs and books that can be helpful. My blog is my personal venture and is selective in its contents. It is not a reflection of the International Society of Genetic Genealogy.

I am the Northwest Regional Coordinator for the International Society of Genetic Genealogy (ISOGG*) and manage twelve DNA Projects and several email lists on Rootsweb and Yahoo. I am available to speak at any function regarding Genetic Genealogy and on writing one's memories and family stories. ......For my DNA Projects, I prefer using Family Tree DNA. You can order a test kit by clicking on the FTDNA logo below.

You are welcome to email me at: aulicino@hevanet.com using the Blog's name in the subject line, if you have any comments or questions.

-------*ISOGG is a non-profit organization designed solely to promote and educate the public about DNA testing in regard to genealogy. Membership is free, but tell them that Emily sent you! See: www.isogg.org --------------

To subscribe, click on POST arrow.

Followers

Presentations

.....Presentations for both the Genetic Genealogy and for the writing sessions are normally two hours, but can be adapted. I prefer an computer projector for with a screen and a table for displaying my DNA book and/or writing booklet......Your group can photocopy the handouts or I will do so for $.05 per side. If speaking within the general area of Portland, Oregon I do not charge for mileage or travel expenses. Outside of the general Portland area, I do require the IRS amount of $.56 per mile. If I need to stay over night, a motel room or staying with a non-smoking female will be necessary......Although, as a member of the International Society of Genetic Genealogists (ISOGG), I cannot ask for a speaker's fee for the Genetic Genealogy presentations, but I can accept an honorarium. This is not the case with the writing classes. $75 is the standard.Email: aulicino@hevanet.com

Recommendations and Compliments

Genetic Genealogy

"Emily Aulicino is one of the most dynamic people I know. Her energy and enthusiasm has helped make Oregon the largest member per capita region in all of ISOGG. Emily’s educator background is apparent and complimentary to her speaking engagements which create a presentation that is easy-to-understand for any novice. Her reputation has made her an immensely popular speaker throughout the Pacific Northwest which has resulted in nationwide requests. Emily is a proven leader who welcomes a challenge. She manages many people and projects with skill and ability that can only be innate. I have the utmost confidence that Emily will excel at any task presented to her and I look forward to many more years working with her."-------Katherine Borges, Director of the International Society of Genetic Genealogy (ISOGG)

Unsolicited Comments:

Barbara in Washington wrote:I just wanted to touch base with you and tell you how impressed I was with your lectures today. They were fun and up, and you were able to explain the DNA process to me in terms that I could understand.

"Memoing" My Memories

130 Topic Booklet for Sale

"Memoing" My Memories - Unsolicited Testimony

Rhonda in Oregon writes:The writing tip you gave us Thursday is great! I went right to my stash of journals (I have trouble journaling, but love the books!), and made a page for every year since my birth year.I’m very excited to start writing my memories down. Thanks again for a fantastic tip!!

Anne in Michigan writes:"So many times I have sat down and tried to write out my life's story. I got so bored with myself that I never got more than a few pages done. This method has totally changed my outlook and has renewed my lifelong interest to write about my life so that my children will have something to remember me by.I am psyched, pumped and ready to go now!”

Beth in Texas writes:“I am finding the topics very helpful in writing about things I would have never thought about before. These topics give me an opportunity not to dwell on the unhappy times in my life, and remember some of the less important, but memorable topics that I'd like to pass on to my children. I'll still write about unhappy times, but they will be sprinkled in with other memories.”

Jan in Kentucky writes:“Emily, you do so very much for so many, and it is so appreciated! You also have broken my writing block, and I appreciate that...if not for you, I don't know that I would have had the heart to return to it. You truly are doing a lot of good with that list of yours and the effects will be known for years and generations for so many. I think sometimes we just need to tell you that.”

Bob in Sherwood, Oregon writes:THANKS to you I started writing my "story" last Friday. If it wasn't for you I probably wouldn't have started it. It's all your fault...You, You, "Inspirator", You! Telling usto write in "pictures". If I started it prior to your presentation it would have begun... "I was born on October 29, 1944 in Jamestown, New York". Needless to say you had a GREAT impact on my writing.

Bill in New Jersey writes:Just a short note to says thanks to you, Emily, for the prompts. I especially like the way in which you write the suggestions to go along with the prompts.

Books About Childhood Memories and Family Stories

As most of you know I seldom read fiction, and as a result, I am interested in books that are historical in nature and/or tell the stories of people's lives. The following list is some books that I have read which are by people I know, people who are related to me, people I have met, and people with whom I've corresponded for a time. Proudly, I have each author's autograph, and I'm beginning to think of this as a new collection/hobby of mine! .

Each of these stories have great struggles and challenges. Some are of childhood while others occurred when the author was an adult. I hope that you will find them interesting as I have. They are truly a slice of our American Life!

Childhood Shadows: The Hidden Story of the Black Dahlia Murder by Mary Pacios

Son of Scarface: A Memoir by the Grandson of Al Capone by Chris W. Knight

Run Jane Run: A True Story of Murder and Courage by Jane Wells

Somehow, We'll Survive: Life in Japan During World War II Through The Eyes of a Young Caucasian Boy by George Sidline

About Me

Emily is available for Presentations regarding Writing Your Family Memories and Childhood Stories.
----- Learn to WRITE ABOUT YOUR CHILDHOOD AND FAMILY MEMORIES using a quick and simple technique. Learn various organizational ideas and writing tips. ------- BOOK FOR SALE on writing your memories at workshops or by mail (Spiral bound; 144 pages on heavy vellum; 130 topics with writing tips and organizational ideas).
Emily is also available to give presentations on Genetic Genealogy. See the following blog for more information: http://genealem-geneticgenealogy.blogspot.com/
--------- EMAIL for further details on either topic:
aulicino@hevanet.com

LINKEDIN

International Society of Genetic Genealogists

Family Tree DNA - Click Logo to order a test

To Order at DNA test kit from FTDNA through this blog

...1. Click on the FTDNA icon search button (above)....2. Enter the _(your surname here)_ surname in the upper right where it says: SEARCH...3. On the next page, click on the surname you chose in #2....4. Follow any instructions. Scroll to the bottom of the page and click on JOIN.

NOTE: If you are not certain there is a DNA project for your surname or if you are only testing your mtDNA (female line), put the name: CAMPANIA in the search field. This is one of my projects, and I will find you an appropriate project when your results arrive...........You want to join through a project to get the cheapest rates.